Variant report

Variant	rs10204958
Chromosome Location	chr2:39242703-39242704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39237020..39239213-chr2:39240112..39243107,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10165968	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs10169337	0.86[CHB][hapmap]
rs10172085	0.81[ASN][1000 genomes]
rs10184015	0.85[ASN][1000 genomes]
rs10190377	0.93[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs10201980	0.87[CHD][hapmap]
rs10205802	0.86[CHB][hapmap]
rs10206751	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs1037495	0.86[CHB][hapmap]
rs12622969	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs13031871	0.80[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs13033392	0.83[ASN][1000 genomes]
rs1377863	0.84[ASN][1000 genomes]
rs1377864	0.93[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1454223	0.81[CHD][hapmap]
rs1470914	0.93[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1470915	0.87[CHD][hapmap]
rs1869513	0.84[CHD][hapmap]
rs2060988	0.93[CHB][hapmap]
rs2123882	0.85[ASN][1000 genomes]
rs2168043	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap]
rs2278914	0.81[CHD][hapmap]
rs2373497	0.93[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs2888586	0.84[JPT][hapmap]
rs297120	0.93[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs297124	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs297134	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs297136	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs297142	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs297144	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs297151	0.93[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap]
rs297152	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs3796038	0.93[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs4670902	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs6713281	0.87[CHD][hapmap]
rs6725356	0.81[CHD][hapmap]
rs6758330	0.86[CHB][hapmap]
rs7577088	0.81[CHD][hapmap]
rs7607509	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10204958	SOS1	cis	lymphoblastoid	seeQTL
rs10204958	SOS1	cis	multi-tissue	Pritchard
rs10204958	DHX57	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39211000-39247600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:39213400-39251200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39213400-39259800	Weak transcription	Right Ventricle	heart
4	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
5	chr2:39217600-39244200	Strong transcription	Primary B cells from cord blood	blood
6	chr2:39219000-39259200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:39219200-39244000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:39227600-39303400	Weak transcription	Colonic Mucosa	Colon
9	chr2:39229000-39251400	Weak transcription	Fetal Heart	heart
10	chr2:39229800-39293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:39230200-39243600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:39231600-39244400	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr2:39232200-39242800	Strong transcription	Liver	Liver
14	chr2:39232400-39242800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:39232600-39300000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:39235400-39249600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:39235400-39312000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:39235600-39247600	Weak transcription	HSMMtube	muscle
19	chr2:39235600-39251800	Weak transcription	NHEK	skin
20	chr2:39235600-39259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:39235600-39259800	Weak transcription	Spleen	Spleen
22	chr2:39235600-39293200	Weak transcription	Fetal Brain Male	brain
23	chr2:39235600-39295800	Weak transcription	NHLF	lung
24	chr2:39235600-39298200	Weak transcription	Small Intestine	intestine
25	chr2:39235600-39327800	Weak transcription	Esophagus	oesophagus
26	chr2:39235800-39249600	Weak transcription	Thymus	Thymus
27	chr2:39235800-39257800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:39235800-39284000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:39235800-39293600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:39236000-39247600	Weak transcription	Left Ventricle	heart
31	chr2:39236000-39249600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:39236000-39260000	Weak transcription	Hela-S3	cervix
33	chr2:39236000-39295600	Weak transcription	Aorta	Aorta
34	chr2:39236000-39295800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:39236000-39305600	Weak transcription	Gastric	stomach
36	chr2:39236200-39305600	Weak transcription	Lung	lung
37	chr2:39236400-39263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr2:39236800-39242800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:39236800-39245600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:39237000-39260200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr2:39237600-39257600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:39237800-39249800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:39238400-39256400	Weak transcription	Fetal Intestine Small	intestine
44	chr2:39238400-39260600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:39238600-39256400	Weak transcription	Fetal Stomach	stomach
46	chr2:39239200-39249600	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:39239400-39245600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr2:39239400-39249600	Weak transcription	HUVEC	blood vessel
49	chr2:39239400-39254600	Weak transcription	Brain Germinal Matrix	brain
50	chr2:39240400-39249400	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links